1c0k: Difference between revisions

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{{Seed}}
[[Image:1c0k.png|left|200px]]


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==CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE==
The line below this paragraph, containing "STRUCTURE_1c0k", creates the "Structure Box" on the page.
<StructureSection load='1c0k' size='340' side='right'caption='[[1c0k]], [[Resolution|resolution]] 1.46&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1c0k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodotorula_toruloides Rhodotorula toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C0K FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.46&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=LAC:LACTIC+ACID'>LAC</scene></td></tr>
{{STRUCTURE_1c0k|  PDB=1c0k  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1c0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0k OCA], [https://pdbe.org/1c0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c0k RCSB], [https://www.ebi.ac.uk/pdbsum/1c0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0k ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c0/1c0k_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1c0k ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Flavin is one of the most versatile redox cofactors in nature and is used by many enzymes to perform a multitude of chemical reactions. d-Amino acid oxidase (DAAO), a member of the flavoprotein oxidase family, is regarded as a key enzyme for the understanding of the mechanism underlying flavin catalysis. The very high-resolution structures of yeast DAAO complexed with d-alanine, d-trifluoroalanine, and l-lactate (1.20, 1.47, and 1.72 A) provide strong evidence for hydride transfer as the mechanism of dehydrogenation. This is inconsistent with the alternative carbanion mechanism originally favored for this type of enzymatic reaction. The step of hydride transfer can proceed without involvement of amino acid functional groups. These structures, together with results from site-directed mutagenesis, point to orbital orientation/steering as the major factor in catalysis. A diatomic species, proposed to be a peroxide, is found at the active center and on the Re-side of the flavin. These results are of general relevance for the mechanisms of flavoproteins and lead to the proposal of a common dehydrogenation mechanism for oxidases and dehydrogenases.


===CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE===
The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.,Umhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12463-8. PMID:11070076<ref>PMID:11070076</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1c0k" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_11070076}}, adds the Publication Abstract to the page
*[[Amino acid oxidase 3D structures|Amino acid oxidase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 11070076 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_11070076}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1C0K is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0K OCA].
[[Category: Rhodotorula toruloides]]
 
[[Category: Diederichs K]]
==Reference==
[[Category: Ghisla S]]
The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation., Umhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S, Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12463-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11070076 11070076]
[[Category: Molla G]]
[[Category: D-amino-acid oxidase]]
[[Category: Pilone MS]]
[[Category: Rhodosporidium toruloides]]
[[Category: Pollegioni L]]
[[Category: Single protein]]
[[Category: Umhau S]]
[[Category: Diederichs, K.]]
[[Category: Welte W]]
[[Category: Ghisla, S.]]
[[Category: Molla, G.]]
[[Category: Pilone, M S.]]
[[Category: Pollegioni, L.]]
[[Category: Umhau, S.]]
[[Category: Welte, W.]]
[[Category: Alpha-beta-alpha motif]]
[[Category: Flavin containing protein]]
[[Category: Oxidoreductase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 20:02:30 2008''

Latest revision as of 10:47, 15 November 2023

CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATECRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE

Structural highlights

1c0k is a 1 chain structure with sequence from Rhodotorula toruloides. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.46Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OXDA_RHOTO This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Flavin is one of the most versatile redox cofactors in nature and is used by many enzymes to perform a multitude of chemical reactions. d-Amino acid oxidase (DAAO), a member of the flavoprotein oxidase family, is regarded as a key enzyme for the understanding of the mechanism underlying flavin catalysis. The very high-resolution structures of yeast DAAO complexed with d-alanine, d-trifluoroalanine, and l-lactate (1.20, 1.47, and 1.72 A) provide strong evidence for hydride transfer as the mechanism of dehydrogenation. This is inconsistent with the alternative carbanion mechanism originally favored for this type of enzymatic reaction. The step of hydride transfer can proceed without involvement of amino acid functional groups. These structures, together with results from site-directed mutagenesis, point to orbital orientation/steering as the major factor in catalysis. A diatomic species, proposed to be a peroxide, is found at the active center and on the Re-side of the flavin. These results are of general relevance for the mechanisms of flavoproteins and lead to the proposal of a common dehydrogenation mechanism for oxidases and dehydrogenases.

The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.,Umhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12463-8. PMID:11070076[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. Umhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S. The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation. Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12463-8. PMID:11070076 doi:10.1073/pnas.97.23.12463

1c0k, resolution 1.46Å

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